D. A. Potoyan

Mapping energy landscapes of homopolymeric RNAs via simulated tempering and deep unsupervised learning

The paper maps temperature-dependent conformational free energy landscapes of homopolymeric RNAs using simulations and deep learning, revealing base-specific phase separation propensities.

Temperature-Sensitive Contact Modes Allosterically Gate TRPV3

This study identifies temperature-sensitive residue-residue interactions in TRPV3 using simulations and machine learning, revealing how these contacts allosterically regulate channel gating.

Temperature Sensitive Contacts in Disordered Loops Tune Enzyme I Activity

This study identifies temperature-sensitive contacts in disordered loops of Enzyme I homologs that tune catalytic activity across temperatures.

The interplay of chromatin phase separation and lamina interactions in nuclear organization

This paper develops a field-theoretic model of the nucleus as a multi-phase chromatin condensate to explain dynamic chromatin organization and interactions observed in imaging experiments.

Programmable Viscoelasticity in Protein-RNA Condensates with Disordered Sticker-Spacer Polypeptides

The paper investigates the viscoelastic properties of protein-RNA condensates formed by sticker-spacer polypeptides and shows how sequence composition tunes their mechanical behavior.

Liquid-liquid phase separation driven compartmentalization of reactive nucleoplasm.

The paper constructs a minimalist model of the reactive nucleoplasm to study how gene regulation influences liquid-liquid phase separation and generates heterogeneous gene expression patterns.

Sequence-encoded and Composition-dependent Protein-RNA Interactions Control Multiphasic Condensate Morphologies

The paper shows how competition between protein-RNA interactions drives phase separation into distinct condensate morphologies, determined by stoichiometry and interaction hierarchy.

Phase Transition of RNA-protein Complexes into Ordered Hollow Condensates

This study identifies a new phase of RNA-protein condensates forming hollow vesicles through phase separation, distinct from typical liquid droplets.

Disorder mediated oligomerization of DISC1 proteins revealed by coarse-grained computer simulations.

This study uses coarse-grained simulations to show that conformational heterogeneity and structural disorder influence DISC1 oligomerization, with differences observed between full-length and truncated variants.

Mesoscale liquid model of chromatin recapitulates nuclear order of eukaryotes.

The paper develops a mesoscale liquid model of chromatin to study nuclear organization and dynamics during cell life cycles.